ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1696921
This article is part of the Research TopicAdvancing sugarcane sustainability: Breeding and innovations for climate resilienceView all articles
Differential Gene Expression and Phenotypic Variation Across Tissues Between Saccharum officinarum and S. spontaneum
Provisionally accepted
- 1Fujian Agriculture and Forestry University, Fuzhou, China
- 2Guangdong Academy of Sciences, Guangzhou, China
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Abstract: Modern sugarcane cultivars (Saccharum spp.), predominantly derived from S. officinarum and S. spontaneum, exhibit divergent traits in sugar content, yield, and stress-tolerance. However, little is known about the spatial transcriptional regulation pattern of the differentially expressed genes (DEGs) among tissues in the two Saccharum species. This study aimed to investigate these genes and according to pathways in leaf, stem, root, and flower tissues using comparative transcriptomic analysis. We identified a broad range of DEGs ranging from 24,469 to 34,198 in four tissues from Badila (S. officinarum) and Ledong2 (S. spontaneum) clones. Thirty-one DEGs involved in abscisic acid (ABA) biosynthesis were identified in root, suggesting differences in ABA content within root tissues between the two clones. In stem tissues, a significant number of upregulated DEGs were associated with cell growth and division, alongside plant-type cell wall organization, while abundant downregulated DEGs were linked to stress-response processes, possibly contributing to heterogeneity in stem morphology and stress responses. In leaf tissues, DEGs related to photosynthesis and photorespiration pathways likely influenced the variation in plant biomass and sucrose content between Badila and Ledong2. Key DEGs, including LHY, PRR7, and GI, associated with circadian rhythms and photoperiodic pathway, were identified in flower tissues, providing evidence to explain the discrepancy in flowering time between two clones. Collectively, the differential regulation of genes across four tissues may contribute to illustrating the divergence of agronomic traits and stress responses in both Saccharum species, offering a valuable foundation for the genetic improvement of sugarcane cultivation and stress resilience.
Keywords: Differentially expressed genes, Phenotypic variation, Saccharum officinarum, Saccharum spontaneum, transcriptome analysis, tissue-specific expression
Received: 01 Sep 2025; Accepted: 10 Oct 2025.
Copyright: © 2025 Wang, Sun, Chen, Zhou, Qin, Zhang, Chen and Gao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: San-Ji Gao, gaosanji@fafu.edu.cn
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